DRAFT Fix tooltip rebase bt5

api/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vitro-api</artifactId>
-    <version>1.14.1-SNAPSHOT</version>
+    <version>1.15.1-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vitro-project</artifactId>
-        <version>1.14.1-SNAPSHOT</version>
+        <version>1.15.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -88,7 +88,7 @@
         <dependency>
             <groupId>org.vivoweb</groupId>
             <artifactId>vitro-dependencies</artifactId>
-            <version>1.14.1-SNAPSHOT</version>
+            <version>1.15.1-SNAPSHOT</version>
             <type>pom</type>
         </dependency>
         <dependency>

api/src/main/java/edu/cornell/mannlib/vitro/webapp/auth/checks/SparqlSelectQueryResultsChecker.java

@@ -46,7 +46,7 @@ public static boolean sparqlSelectQueryResultsContain(Check check, Authorization
         AccessObject ao = ar.getAccessObject();
         Model m = ao.getModel();
         if (m == null) {
-            log.debug("SparqlQueryContains model is not provided");
+            log.error("Model not provided");
             return false;
         }
 
@@ -116,10 +116,11 @@ private static Set<String> getSparqlSelectResults(Model model, String profileUri
             AuthorizationRequest ar) {
         HashMap<String, Set<String>> queryMap = QueryResultsMapCache.get();
         String queryMapKey = createQueryMapKey(profileUri, queryTemplate, ar);
+        HashSet<String> results = new HashSet<>();
         if (queryMap.containsKey(queryMapKey)) {
-            return queryMap.get(queryMapKey);
+            results.addAll(queryMap.get(queryMapKey));
+            return results;
         }
-        Set<String> results = new HashSet<>();
         ParameterizedSparqlString pss = new ParameterizedSparqlString();
         pss.setCommandText(queryTemplate);
         setVariables(profileUri, ar, pss);
@@ -140,7 +141,9 @@ private static Set<String> getSparqlSelectResults(Model model, String profileUri
             queryExecution.close();
         }
         debug("query results: " + results);
-        queryMap.put(queryMapKey, results);
+        Set<String> queryMapValue = new HashSet<>();
+        queryMapValue.addAll(results);
+        queryMap.put(queryMapKey, queryMapValue);
         QueryResultsMapCache.update(queryMap);
         return results;
     }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/IndividualListController.java

@@ -8,6 +8,7 @@
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 
 import javax.servlet.annotation.WebServlet;
 
@@ -28,6 +29,8 @@
 import edu.cornell.mannlib.vitro.webapp.i18n.I18n;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineException;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchQuery;
+import edu.cornell.mannlib.vitro.webapp.search.controller.SearchFilter;
+import edu.cornell.mannlib.vitro.webapp.search.controller.SearchFiltering;
 import edu.cornell.mannlib.vitro.webapp.utils.searchengine.SearchQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividual;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividualBuilder;
@@ -188,15 +191,15 @@ private static IndividualListResults buildAndExecuteVClassQuery(List<String> cla
 		boolean languageFilter = Boolean.valueOf(props.getProperty(LANGUAGE_FILTER_PROPERTY, "false"));
 		IndividualListQueryResults results = buildAndExecuteVClassQuery(classUris, alpha,
 				((languageFilter) ? vreq.getLocale() : null), page, pageSize,
-				vreq.getWebappDaoFactory().getIndividualDao());
+				vreq);
 		IndividualListResults indListResults = getResultsForVClassQuery(results, page, pageSize, alpha, vreq);
 		return indListResults;
 	}
 
     public static IndividualListResults getRandomResultsForVClass(String vclassURI, int page, int pageSize, VitroRequest vreq) {
    	 	try{
             List<String> classUris = Collections.singletonList(vclassURI);
-			IndividualListQueryResults results = buildAndExecuteRandomVClassQuery(classUris, page, pageSize, vreq.getWebappDaoFactory().getIndividualDao());
+			IndividualListQueryResults results = buildAndExecuteRandomVClassQuery(classUris, page, pageSize, vreq);
 	        return getResultsForVClassQuery(results, page, pageSize, "", vreq);
    	 	} catch(Throwable th) {
 	   		log.error("An error occurred retrieving random results for vclass query", th);
@@ -216,9 +219,12 @@ private static IndividualListResults getResultsForVClassQuery(IndividualListQuer
 
     private static IndividualListQueryResults buildAndExecuteVClassQuery(
 			List<String> vclassURIs, String alpha, Locale locale, int page,
-			int pageSize, IndividualDao indDao)
+			int pageSize, VitroRequest vreq)
 			throws SearchEngineException {
+		 IndividualDao indDao = vreq.getWebappDaoFactory().getIndividualDao();
 		 SearchQuery query = SearchQueryUtils.getQuery(vclassURIs, alpha, locale, page, pageSize);
+		 Set<String> currentRoles = SearchFiltering.getCurrentUserRoles(vreq);
+		 SearchFiltering.addDefaultFilters(query, currentRoles);
 		 IndividualListQueryResults results = IndividualListQueryResults.runQuery(query, indDao);
 		 log.debug("Executed search query for " + vclassURIs);
 		 if (results.getIndividuals().isEmpty()) {
@@ -228,9 +234,12 @@ private static IndividualListQueryResults buildAndExecuteVClassQuery(
 	}
 
     private static IndividualListQueryResults buildAndExecuteRandomVClassQuery(
-			List<String> vclassURIs, int page, int pageSize, IndividualDao indDao)
+			List<String> vclassURIs, int page, int pageSize, VitroRequest vreq)
 			throws SearchEngineException {
+		 IndividualDao indDao = vreq.getWebappDaoFactory().getIndividualDao();
 		 SearchQuery query = SearchQueryUtils.getRandomQuery(vclassURIs, page, pageSize);
+		 Set<String> currentRoles = SearchFiltering.getCurrentUserRoles(vreq);
+		 SearchFiltering.addDefaultFilters(query, currentRoles);
 		 IndividualListQueryResults results = IndividualListQueryResults.runQuery(query, indDao);
 		 log.debug("Executed search query for " + vclassURIs);
 		 if (results.getIndividuals().isEmpty()) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/grefine/JSONReconcileServlet.java

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.controller.grefine;
 
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -11,7 +12,6 @@
 import java.util.Map;
 
 import javax.servlet.ServletException;
-import javax.servlet.ServletOutputStream;
 import javax.servlet.annotation.WebServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -70,6 +70,7 @@ protected void doGet(HttpServletRequest req, HttpServletResponse resp)
 			throws ServletException, IOException {
 		super.doGet(req, resp);
 		resp.setContentType("application/json");
+		resp.setCharacterEncoding("UTF-8");
 		VitroRequest vreq = new VitroRequest(req);
 
 		try {
@@ -81,7 +82,7 @@ protected void doGet(HttpServletRequest req, HttpServletResponse resp)
 						.toString() : vreq.getParameter("callback") + "("
 						+ qJson.toString() + ")";
 				// System.out.println("JSONReconcileServlet result: " + responseStr);
-				ServletOutputStream out = resp.getOutputStream();
+				PrintWriter out = resp.getWriter();
 				out.print(responseStr);
 			} else { // metadata
 				String defaultNamespace = null;
@@ -97,7 +98,7 @@ protected void doGet(HttpServletRequest req, HttpServletResponse resp)
 				ObjectNode metaJson = getMetadata(req, resp, defaultNamespace, defaultTypeList, serverName, serverPort);
 				String callbackStr = (vreq.getParameter("callback") == null) ? ""
 						: vreq.getParameter("callback");
-				ServletOutputStream out = resp.getOutputStream();
+				PrintWriter out = resp.getWriter();
 				out.print(callbackStr + "(" + metaJson.toString() + ")");
 			}
 		} catch (Exception ex) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java

@@ -2,6 +2,9 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import static edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph.sparqlNode;
+import static edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph.sparqlNodeDelete;
+
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -565,25 +568,45 @@ private static List<Statement> sort(List<Statement> stmts) {
 
     private static void addStatementPatterns(List<Statement> stmts,
     		StringBuffer patternBuff, boolean whereClause) {
+        Set<String> lines = new HashSet<>();
         for(Statement stmt : stmts) {
             Triple t = stmt.asTriple();
-            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
-            patternBuff.append(" ");
-            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));
-            patternBuff.append(" ");
-            patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getObject(), null));
-            patternBuff.append(" .\n");
+            String lineWithoutVars = getLine(t, false);
+            if (lines.contains(lineWithoutVars)) {
+                continue;
+            } else {
+                lines.add(lineWithoutVars);
+            }
+            patternBuff.append(getLine(t, true));
             if (whereClause) {
                 if (t.getSubject().isBlank()) {
                     patternBuff.append("    FILTER(isBlank(").append(
-                    		SparqlGraph.sparqlNodeDelete(t.getSubject(), null)).append(")) \n");
+                    		sparqlNodeDelete(t.getSubject(), null)).append(")) \n");
                 }
                 if (t.getObject().isBlank()) {
                     patternBuff.append("    FILTER(isBlank(").append(
-                    		SparqlGraph.sparqlNodeDelete(t.getObject(), null)).append(")) \n");
+                    		sparqlNodeDelete(t.getObject(), null)).append(")) \n");
                 }
             }
         }
     }
 
+    private static String getLine(Triple t, boolean createBlankNodeVariables) {
+        if (createBlankNodeVariables) {
+            return sparqlNodeDelete(t.getSubject(), null) +
+                    " " +
+                    sparqlNodeDelete(t.getPredicate(), null) +
+                    " " +
+                    sparqlNodeDelete(t.getObject(), null) +
+                    " .\n";
+        } else {
+            return sparqlNode(t.getSubject(), null) +
+                    " " +
+                    sparqlNode(t.getPredicate(), null) +
+                    " " +
+                    sparqlNode(t.getObject(), null) +
+                    " .\n";
+        }
+    }
+
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultObjectPropertyFormGenerator.java

@@ -2,15 +2,14 @@
 
 package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators;
 
-import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.LANGUAGE_NEUTRAL;
-import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.POLICY_NEUTRAL;
 import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames.DISPLAY;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import javax.servlet.http.HttpSession;
 
@@ -45,6 +44,7 @@
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchResponse;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchResultDocumentList;
 import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
+import edu.cornell.mannlib.vitro.webapp.search.controller.SearchFiltering;
 import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils.EditMode;
 
@@ -187,7 +187,7 @@ private boolean tooManyRangeOptions(VitroRequest vreq, HttpSession session ) thr
     	if(types.size() == 0 ){
     		types.add(VitroVocabulary.OWL_THING);
     	}
-
+    	Set<String> currentRoles = SearchFiltering.getCurrentUserRoles(vreq);
     	long count = 0;
     	for( String type:types){
     		//search query for type count.
@@ -198,6 +198,7 @@ private boolean tooManyRangeOptions(VitroRequest vreq, HttpSession session ) thr
     			query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type);
     		}
     		query.setRows(0);
+    		SearchFiltering.addDefaultFilters(query, currentRoles);
     		SearchResponse rsp = searchEngine.query(query);
     		SearchResultDocumentList docs = rsp.getResults();
     		long found = docs.getNumFound();
@@ -549,9 +550,9 @@ public void addFormSpecificDataForAC(EditConfigurationVTwo editConfiguration, Vi
 			String objectLabel = EditConfigurationUtils.getObjectIndividual(vreq).getName();
 			formSpecificData.put("objectLabel", objectLabel);
 		}
-
+		Set<String> currentRoles = SearchFiltering.getCurrentUserRoles(vreq);
 		//TODO: find out if there are any individuals in the classes of objectTypes
-		formSpecificData.put("rangeIndividualsExist", rangeIndividualsExist(types) );
+		formSpecificData.put("rangeIndividualsExist", rangeIndividualsExist(types, currentRoles) );
 
 		formSpecificData.put("sparqlForAcFilter", getSparqlForAcFilter(vreq));
 		if(customErrorMessages != null && !customErrorMessages.isEmpty()) {
@@ -561,7 +562,7 @@ public void addFormSpecificDataForAC(EditConfigurationVTwo editConfiguration, Vi
 		editConfiguration.setFormSpecificData(formSpecificData);
 	}
 
-	private Object rangeIndividualsExist(List<VClass> types) throws SearchEngineException {
+	private Object rangeIndividualsExist(List<VClass> types, Set<String> currentRoles) throws SearchEngineException {
 		SearchEngine searchEngine = ApplicationUtils.instance().getSearchEngine();
 
     	boolean rangeIndividualsFound = false;
@@ -570,6 +571,7 @@ private Object rangeIndividualsExist(List<VClass> types) throws SearchEngineExce
     		SearchQuery query = searchEngine.createQuery();
     		query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type.getURI());
     		query.setRows(0);
+    		SearchFiltering.addDefaultFilters(query, currentRoles);
 
     		SearchResponse rsp = searchEngine.query(query);
     		SearchResultDocumentList docs = rsp.getResults();